ontology:OntologyTools

From NITRC Wiki

Protege

- Protege v3.4.x+ (OWL v1.0 based),

- Protege 4 (OWL v1.1 based), http://protegewiki.stanford.edu/index.php/ Protege4UserDocs .

BioNotes

BioNotes is a pilot project that Dilvan undertook to create the marginal notes capability. It has been picked up by the BioPortal development team and will be incorporated (though re-engineered) into BioPortal, appearing likely in late summer. (content from Daniel Rubin)

TOP

TOP (Terminology Open Portal) arose out of the desire from NCI to install BioPortal locally and modify it and release modified or new components to the community of similar users. NCBO BioPortal development is coordinating closely with TOP so that the community knows "BioPortal" to be just one animal. (content from Daniel Rubin)

Collaborative Protege

Collaborative Protege is for ontology DEVELOPERS (remember, BioPortal is about disseminating ontologies to the world and collecting feedback, hosting mappings, etc, but it's not about creating or editing the original ontologies--that's what you need something like Protege or Collaborative Protege). The different between it and Protege as you know it is support for ontology development workflow. The potential confusion is that it too includes "marginal notes", but the use case is for communication amongst ontology developers in their workflow. (content from Daniel Rubin)

You can certainly look at Dilvan's latest release, but please remember that this is not going to be a production product. It will give you a sense for functionality that will be in the next release of BioPortal. Your feedback will be critical in summer when that release happens. There is a feedback link in BioPortal, and of course you can always email us. (content from Daniel Rubin)

SWRL

SWRL: A Semantic Web Rule Language Combining OWL and RuleML . See http://www.w3.org/Submission/SWRL/

RDFScape

RDFScape (v0.4) is software that makes it possible to read, query, browse and visualize RDF/OWL ontologies within the popular systems biology software Cytoscape. See http://www.bioinformatics.org/rdfscape/ & http://www.cytoscape.org

Unlike other ontology related features of Cytoscape, RDFScape treats ontology through a reasoner, where both standard entailments (OWL,RDF... with a choice of Jena reasoners or Pellet) and custom inference rules can be computed.

This means original ontologies can be "interpreted" within cytoscape. For instance, a biopax representation of pathways in humans (say from PathwayCommons/Reactome) can be abstracted and visualized as an interaction network, or as a cause-effect network (once a concept of cause-effect is defined through axioms).

Apart from this, it offers query possibility within Cytoscape (SPARQL and others) and a nice visualization tool for ontologies. It also offers an interactive ontology browsing function (the rdf network can be interactively expanded) and the possibility to define query as graph patterns (visually).

(Content from Andrea Splendiani)

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